It's expected that the basic water bottles once used on a dirt block to turn them into a mud block will retrieve an empty glass bottle; but that should not happen when splash and lingering are being used.

To try this by yourselves just take a stack of splash water bottles and another stack of lingering water bottles and once you're close enough to the dirt bock to see its hitbox use on them on it to turn it into mud and note that empty water bottles are being stacked in the inventory.